There has been a remarkable increase in prescription rates of antipsychotics in children and adolescents in recent years. Their side effects are a neglected area of research in this population, despite its vulnerability. In this cross-sectional study, we compared the presence of side effects in 60 children and adolescents who had taken antipsychotic medication for less than 1 month and 66 who had been receiving treatment with antipsychotics for more than 12 months. Mean age for the total sample was 15.62 years (SD 1.85). Groups did not differ in age, gender, or diagnosis. A total of 21.7% of short-term treatment group patients and 37.9% of longer-term treatment group patients presented mild dyskinetic movements (p = 0.004). Hyperprolactinemia was present in 78.6% and 48.5% in the short-term and longer-term treatment groups, respectively. Body mass index (p < 0.001), cholesterol levels (p < 0.001), and low-density lipoprotein-cholesterol (LDL-C) (p = 0.018) were higher in the longer-term treatment group. The use of these drugs in these populations merits careful scrutiny.